You'll want to use NGSUtil's bamutils tool, specifically with -excludebed.

But, id recommend you dont :P
The BAM format is to store highly compressed alignment data. You should treat them like raw, virgin data, without normalization/filtering tweaks here and there to get it into shape.
All that kind of intersection stuff should be done on processed signal data - wigs and bedgraphs, etc - where its much easier to have multiple versions of things and to just dump it all and start afresh from the .bam if you have to.

Just to clarify, I used -
samtools view in.sorted.bam -b -h -o inRegions.bam -U outRegions.bam "chr:start-stop"...
So here the -o file excludes the regions "chr:start-stop" and has the rest, but the -U file only retains the "chr:start-stop"? Thank you for your help!